Judging is exactly what he is doing.
The judicial branch has the power to interpret laws written by the legislative branch. The U.S. Patent Act does not specify software as patentable. Since the legislative branch has not amended that act to be more specific, with regard to software, it is up to the judicial branch to interpret. Even the 2010 Bilski v. Kappos rulling by the US Supreme Court left many questions unanswered on what is patentable or not with regard to software.
In case you were unaware, this is what title 35, Section 101 of the United States Code says about what is patentable
35 U.S.C. 101 Inventions patentable.
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
If you are curious about the history of the courts conflicted rulings on what is patentable with regard to software I recommend you check out this link: http://www.bitlaw.com/software-patent/bilski-and-software-patents.html